Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Increasingly evidences suggest that long intergenic ncRNAs (lincRNAs) are developmentally regulated and play important roles in development and stress responses of plants. However, identification of lincRNAs in wheat is still limited comparing with functional gene expression. The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese Pst race CYR31 and Bgt race E09 at 1, 2, and 3 days post-inoculation was recapitulated to detect the lincRNAs. Here, 283 differential expressed lincRNAs were identified from 58218 putative lincRNAs, which account for 31.2 % of transcriptome. Of which, 254 DE-LincRNAs responded to the Bgt stress, and 52 lincRNAs in Pst. Among them, 1328 SnRNP motifs (sm sites) were detected and showed RRU4–11RR sm site element and consensus RRU1–9VU1–7RR SnRNP motifs, where the total number of uridine was more than 3 but less than 11. Additionally, 101 DE-lincRNAs were predicted as targets of miRNA by psRNATarget, while 5 target mimics were identified using target mimicry search in TAPIR. Taken together, our findings indicate that the lincRNA of wheat responded to Bgt and Pst stress and played important roles in splicesome and inter-regulating with miRNA. The sm site of wheat showed a more complex construction than that in mammal and model plant. The mass sequence data generated in this study provide a cue for future functional and molecular research on wheat–fungus interactions.

The NAM, ATAF1/2, and CUC2 (NAC) transcription factors (TFs) constitute the largest plant-specific TF superfamily, and play important roles in various physiological processes, including stress responses. Stripe rust and powdery mildew are the most damaging of the fungal diseases that afflict wheat (Triticum aestivum L.). However, studies on Triticum aestivum NAC (TaNAC)s’ role in resistance to the two diseases are still limited, especially in an overall comparative analysis of TaNACs responding or not to fungal stress. In the present study, 186 TaNAC transcripts were obtained from the resistant hexaploid wheat line N9134 under fungal stress, and 180 new transcripts were submitted to GenBank. Statistical results show that 35.1% (54/154) of TaNAC genes responded to stripe rust and powdery mildew in the seedling stage. “Abnormal” coding transcripts of differentially expressed (DE)-TaNAC genes in wheat responding to fungal stress were found in a significantly higher proportion (24/117 vs. 8/69, p = 0.0098) than in non-DE-NACs. This hinted that the alternative splicing of TaNAC genes was active in transcriptional or post-transcriptional regulation during plant-pathogen interactions. Full-length NAC proteins were classified into nine groups via phylogenetic analysis. Multiple-sequence alignment revealed diversity in the C-terminal structural organization, but the differentially expressed gene (DEG)-encoding proteins enriched in Subgroups VI and VII were conserved, with WV[L/V]CR amino acid residues in Motif 7 following the NAM domain. Our data that showed TaNAC TFs responded to fungal disease, which was affected by expression levels and by the regulation of multifarious transcript variants. These data for TaNAC responses to stripe rust and/or powdery mildew and their numerous structural variants provide a good resource for NAC function–mechanism analysis in the context of biotic-stress tolerance in wheat.

INDETERMINATE DOMAIN (IDD) transcription factors are plant-specific regulators essential for plant development and stress adaptation. As a globally important staple crop, common wheat (Triticum aestivum L.) is frequently threatened by fungal diseases such as powdery mildew and stripe rust. To date, however, the IDD gene family in wheat has not been systematically characterized, and its roles in biotic stress responses remain unclear. In this study, we performed genome-wide identification and a comprehensive analysis of the TaIDD gene family. A total of 41 TaIDD genes were identified, which were unevenly distributed across 15 chromosomes and divided into four phylogenetic groups. Synteny and selective pressure analyses demonstrated that segmental duplication was the main driver of family expansion and that TaIDD genes underwent strong purifying selection during evolution. Cis-acting element analysis revealed abundant hormone- and stress-related elements in their promoter regions. Transcriptome and RT-qPCR analyses indicated that TaIDD genes exhibited distinct expression patterns under abiotic and biotic stress. Notably, TaIDD13, TaIDD19, TaIDD27, TaIDD37, TaIDD39, and TaIDD41 were significantly induced by multiple fungal pathogens, suggesting their potential involvement in stress-responsive pathways that may be related to disease resistance. Subcellular localization analysis further confirmed that TaIDD39 was exclusively localized in the nucleus, consistent with its function as a transcriptional regulator. Our findings provide insights into the evolutionary characteristics and stress-response mechanisms of TaIDD genes and highlight TaIDD39 and other potential candidates that may serve as valuable resources for wheat molecular breeding to enhance broad-spectrum disease resistance and stress tolerance.